Atomistry » Calcium » PDB 7vmk-7wa0 » 7vpf
Atomistry »
  Calcium »
    PDB 7vmk-7wa0 »
      7vpf »

Calcium in PDB 7vpf: Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4

Protein crystallography data

The structure of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4, PDB code: 7vpf was solved by H.H.Park, J.H.Lee, S.Kwon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.82 / 2.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 141.932, 141.932, 76.701, 90, 90, 120
R / Rfree (%) 21.4 / 27.1

Other elements in 7vpf:

The structure of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 (pdb code 7vpf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4, PDB code: 7vpf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7vpf

Go back to Calcium Binding Sites List in 7vpf
Calcium binding site 1 out of 2 in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:126.7
occ:1.00
OE2 A:GLU247 2.4 119.1 1.0
OE1 A:GLU247 2.4 128.8 1.0
CD A:GLU247 2.7 110.0 1.0
CE1 A:HIS203 3.0 105.3 1.0
OE2 A:GLU142 3.3 90.7 1.0
ND1 A:HIS203 3.4 116.2 1.0
SG A:CYS67 3.6 105.8 1.0
ZN A:ZN302 3.8 200.5 1.0
OE1 A:GLU142 3.8 114.7 1.0
CD A:GLU142 3.9 93.7 1.0
ND2 A:ASN13 3.9 79.8 1.0
NE2 A:HIS203 4.1 76.1 1.0
CG A:GLU247 4.1 97.7 1.0
CG1 A:VAL103 4.5 65.6 1.0
CG A:HIS203 4.6 86.0 1.0
CB A:CYS67 4.7 72.2 1.0
CB A:GLU247 4.7 95.1 1.0
OE2 A:GLU245 4.8 95.9 1.0
CG A:ASN13 4.8 84.6 1.0
CZ2 A:TRP40 4.9 82.0 1.0
CD2 A:HIS203 4.9 74.4 1.0
CG2 A:VAL103 5.0 83.3 1.0
OD1 A:ASN13 5.0 73.2 1.0

Calcium binding site 2 out of 2 in 7vpf

Go back to Calcium Binding Sites List in 7vpf
Calcium binding site 2 out of 2 in the Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:133.5
occ:1.00
OE2 B:GLU247 2.4 119.2 1.0
OE1 B:GLU247 2.5 115.5 1.0
CD B:GLU247 2.8 107.1 1.0
OE2 B:GLU142 2.8 99.3 1.0
ZN B:ZN301 2.9 175.0 1.0
CE1 B:HIS203 3.2 102.9 1.0
ND1 B:HIS203 3.5 99.1 1.0
SG B:CYS67 3.7 98.3 1.0
CD B:GLU142 3.8 101.4 1.0
OE1 B:GLU142 4.0 125.5 1.0
CG B:GLU247 4.3 94.7 1.0
CG1 B:VAL103 4.4 64.3 1.0
ND2 B:ASN13 4.4 81.0 1.0
NE2 B:HIS203 4.5 84.2 1.0
CZ2 B:TRP40 4.8 89.2 1.0
CG B:HIS203 4.8 84.2 1.0
CB B:GLU247 4.9 93.8 1.0

Reference:

S.Kwon, H.J.Ha, Y.J.Kang, J.H.Sung, J.Hwang, M.J.Lee, J.H.Lee, H.H.Park. Crystal Structure of A Novel Putative Sugar Isomerase From the Psychrophilic Bacterium Paenibacillus Sp. R4. Biochem.Biophys.Res.Commun. V. 585 48 2021.
ISSN: ESSN 1090-2104
PubMed: 34784551
DOI: 10.1016/J.BBRC.2021.11.026
Page generated: Thu Jul 10 02:02:23 2025

Last articles

Ca in 9JSG
Ca in 9JSF
Ca in 9JOB
Ca in 9JOA
Ca in 9JJE
Ca in 9IV8
Ca in 9JLM
Ca in 9J34
Ca in 9JJF
Ca in 9IIV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy